W660Rose Genome Sequencing Initiative: Challenges and Benefits
Time: 1:55 PM
IRHS-INRA Angers, France : Fabrice FOUCHER, Latifa HAMAMA, Laurence HIBRAND-SAINT-OYANT, Soulaiman SAKR.
LIPM-INRA Toulouse, Castanet-Tolosan, France : Jérôme GOUZY, Sébastien CARRÈRE, Ludovic LEGRAND, Erika SALLET.
CEA-IG-Genoscope-CNS, Évry, France: Patrick WINCKER, Arnaud LEMAINQUE, Jean-Marc AURY, Arnaud COULOUX, Amin MADOUI.
URGI-INRA Versailles, Versailles, France : Nathalie CHOISNE, Hadi QUESNEVILLE.
Université St Étienne, France : Sylvie BAUDINO, Sandrine MOJA, Jean-Claude CAISSARD.
Université Aix Marseille, France : Manuel LE BRIS, Benjamin GOVETTO.
GDEC-INRA, Clermont-Ferrand, France : Jérôme SALSE.
Paris-Sud University, Orsay, France : Moussa BENHAMED.
ILVO, Melle, Belgium : Katrijn VAN LAERE, Tom RUTTINK, Jan DE RIEK.
WUR, Wageningen, Netherlands : Rene SMULDERS, Paul ARENS.
Texas A&M University, College Station, TX, USA : David BYRNE.
Leibnitz University, Hannover, Germany : Thomas DEBENER.
Hebrew University of Jerusalem, Israel : Dani ZAMIR.
Chinese Academy of Agricultural Science, Beijing, China : Shu-Hua YANG.
Huazhong Agricultural University, Wuhan, China : Xiaopeng FU.
Yunnan Academy of Agricultural Sciences, Kunming, China : Huijun YAN, Kaixue TANG.
University of Minnesota, Saint Paul, MN, USA : Stan HOKANSON.
ABSTRACT : Roses are of high symbolic value and have great cultural importance worldwide. The rose is well suited to be an original model for woody ornamental species as it has relatively small genome size (560Mbp) and short life cycle for a perennial woody plant. Several characters, such as recurrent blooming, flower morphogenesis, scent… are of high economic importance. During the past years, we generated molecular, genomics and biotechnology tools such as an efficient genetic transformation protocol and a database of Rosa expressed genes with thorough annotation and an overview of gene expression patterns in a variety of tissues, conditions and developmental stages; the latest represented a valuable prerequisite to the rose genome sequencing. We have undertaken the genome sequencing of the diploid Rosa chinensis cv. ‘Old Blush’, an ancestor of modern roses that contributed several major characters. We generated and assembled a first draft genome sequence for this cultivar. However, its relatively high heterozygosity hampered high quality genome assembly with 15,938 scaffolds and a N50 of about 230kb. To overcome this difficulty, we have generated and sequenced a R. chinensis homozygous tissue (line HzRc-RDP12) using ‘Old Blush’ as starting material. The availability of this homozygous material yielded high quality genome assembly with reduced number of scaffolds and a N50 of about 1Mb. The combination of the extracted homozygous genome, of high contiguity, and the natural heterozygous genome leads to an almost complete diploid assembly, with the full allele set of the sequenced individual. We also developed a high-density genetic map based on SNP markers (68k rose Axiom Array) using the F1 progeny (151 individuals) from a cross between ‘Old Blush’ and R. wichurana. The ‘Old Blush’ map contains 5635 SNP markers on 7 linkage groups. This genetic map is currently being used to build the rose genome pseudomolecules.
The availability of the rose genome sequence will be of great help for discovering the molecular and genetic mechanisms controlling many traits in Rosa spp. and likely in other Rosaceae species.